4LXC

The antimicrobial peptidase lysostaphin from Staphylococcus simulans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R77pdb entries 1R77, 2B0P
experimental modelPDB 2B0Ppdb entries 1R77, 2B0P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.1 M MES and 1.6 M magnesium sulphate, 2 mM tetraglycine phosphinic acid. EDTA and ammonium sulphate as additives improved crystal quality, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
8.2985.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 282.013α = 90
b = 282.013β = 90
c = 282.013γ = 90
Symmetry
Space GroupP 43 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.5501000.2950.29517.3436.4486934869336.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.591000.9080.9085.3437.93539

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entries 1R77, 2B0P3.547.67486894868924351000.268730.267770.28684RANDOM40.566
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.969
r_dihedral_angle_3_deg17.977
r_dihedral_angle_4_deg9.819
r_dihedral_angle_1_deg6.457
r_angle_other_deg4.421
r_angle_refined_deg1.193
r_symmetry_vdw_other0.252
r_nbd_other0.231
r_symmetry_vdw_refined0.225
r_nbd_refined0.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.969
r_dihedral_angle_3_deg17.977
r_dihedral_angle_4_deg9.819
r_dihedral_angle_1_deg6.457
r_angle_other_deg4.421
r_angle_refined_deg1.193
r_symmetry_vdw_other0.252
r_nbd_other0.231
r_symmetry_vdw_refined0.225
r_nbd_refined0.211
r_nbtor_refined0.195
r_metal_ion_refined0.182
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.142
r_nbtor_other0.118
r_chiral_restr0.066
r_gen_planes_other0.035
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7540
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms49

Software

Software
Software NamePurpose
CBFlibdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling